EzCatDB: S00169

DB codeS00169
RLCP classification5.20.1710000.530
CATH domainDomain 12.160.20.10Catalytic domain
E.C.4.2.2.2
CSA2pec

CATH domainRelated DB codes (homologues)
2.160.20.10S00168,S00171,S00546,S00837,S00170,D00803

Enzyme Name
Swiss-protKEGG

P11073
Protein namePectate lyase Cpectate lyase
polygalacturonic transeliminase
pectic acid transeliminase
polygalacturonate lyase
endopectin methyltranseliminase
pectate transeliminase
endogalacturonate transeliminase
pectic acid lyase
pectic lyase
alpha-1,4-D-endopolygalacturonic acid lyase
PGA lyase
PPase-N
endo-alpha-1,4-polygalacturonic acid lyase
polygalacturonic acid lyase
pectin trans-eliminase
Polygalacturonic acid trans-eliminase
SynonymsEC 4.2.2.2

KEGG pathways
MAP codePathways
MAP00040Pentose and glucuronate interconversions

Swiss-prot:Accession NumberP11073
Entry namePELC_ERWCH
ActivityEliminative cleavage of (1->4)-alpha-D- galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact- 4-enuronosyl groups at their non-reducing ends.
Subunit
Subcellular locationSecreted.
CofactorBinds 1 calcium ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00076C00470C06118C00470
CompoundCalciumPectate4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonatePectate
Typedivalent metal (Ca2+, Mg2+)carboxyl group,polysaccharidecarboxyl group,polysaccharidecarboxyl group,polysaccharide
1airAUnboundUnboundUnboundUnbound
1o88ABound:_CAUnboundUnboundUnbound
1o8dABound:_CAUnboundUnboundUnbound
1o8eABound:_CAUnboundUnboundUnbound
1o8fABound:_CAUnboundUnboundUnbound
1o8gABound:_CAUnboundUnboundUnbound
1o8hABound:_CAUnboundUnboundUnbound
1o8iAUnboundUnboundUnboundUnbound
1o8jABound:_CAUnboundUnboundUnbound
1o8kABound:_CAUnboundUnboundUnbound
1o8lABound:_CAUnboundUnboundUnbound
1o8mAUnboundUnboundUnboundUnbound
1pluAAnalogue:_LUUnboundUnboundUnbound
2pecAUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [8]
pdbCatalytic residuesCofactor-binding residues
1airALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o88ALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8dALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8eALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8fALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8gALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8hALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8iALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8jALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8kALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8lALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1o8mALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
1pluALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)
2pecALYS 190;ARG 218
ASP 131;GLU 166;ASP 170(Calcium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.722
[4]p.361-363
[5]p.163
[6]p.90
[8]p.1086-1088
[10]Fig.2, p.8763-8765
[11]p.1790-1791
[13]p.1012-1013

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID93276270
PubMed ID8502994
JournalScience
Year1993
Volume260
Pages1503-7
AuthorsYoder MD, Keen NT, Jurnak F
TitleNew domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
Related Swiss-protP11073
[2]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID95360717
PubMed ID7634076
JournalNat Struct Biol
Year1994
Volume1
Pages717-23
AuthorsPickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J
TitleThe structure of Bacillus subtilis pectate lyase in complex with calcium.
Related PDB1bn8
Related Swiss-protP39116
[3]
CommentsX-ray crystallography
PubMed ID7896002
JournalFASEB J
Year1995
Volume9
Pages335-42
AuthorsYoder MD, Jurnak F
TitleProtein motifs. 3. The parallel beta helix and other coiled folds.
Related PDB2pec
[4]
CommentsX-ray crystallography
PubMed ID12228363
JournalPlant Physiol
Year1995
Volume107
Pages349-364
AuthorsYoder MD, Jurnak F
TitleThe Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
Related PDB1plu
[5]
PubMed ID8870663
JournalBiochem J
Year1996
Volume319
Pages159-64
AuthorsRao MN, Kembhavi AA, Pant A
TitleRole of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
JournalPlant Physiol
Year1996
Volume111
Pages73-92
AuthorsLietzke SE, Scavetta RD, Yoder MD, Jurnak FA
TitleThe refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
Related PDB1air
Related Swiss-protP11073
[7]
PubMed ID9195887
JournalStructure
Year1997
Volume5
Pages677-89
AuthorsMayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkins J
TitleTwo crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases.
[8]
PubMed ID10368179
JournalPlant Cell
Year1999
Volume11
Pages1081-92
AuthorsScavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Kester HC, Visser J, Jurnak F
TitleStructure of a plant cell wall fragment complexed to pectate lyase C.
[9]
PubMed ID11123920
JournalBiochemistry
Year2000
Volume39
Pages15932-43
AuthorsKamen DE, Griko Y, Woody RW
TitleThe stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
[10]
PubMed ID10922032
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages8762-9
AuthorsHerron SR, Benen JA, Scavetta RD, Visser J, Jurnak F
TitleStructure and function of pectic enzymes: virulence factors of plant pathogens.
[11]
PubMed ID11717490
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1786-92
AuthorsAkita M, Suzuki A, Kobayashi T, Ito S, Yamane T
TitleThe first structure of pectate lyase belonging to polysaccharide lyase family 3.
[12]
PubMed ID11256961
JournalBiochem J
Year2001
Volume355
Pages167-77
AuthorsMcKie VA, Vincken JP, Voragen AG, van den Broek LA, Stimson E, Gilbert HJ
TitleA new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
[13]
PubMed ID12037303
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages1008-15
AuthorsThomas LM, Doan CN, Oliver RL, Yoder MD
TitleStructure of pectate lyase A: comparison to other isoforms.
Related PDB1jrg,1jta
[14]
PubMed ID11926835
JournalBiochemistry
Year2002
Volume41
Pages4724-32
AuthorsKamen DE, Woody RW
TitleIdentification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
[15]
PubMed ID11926834
JournalBiochemistry
Year2002
Volume41
Pages4713-23
AuthorsKamen DE, Woody RW
TitleFolding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
[16]
PubMed ID12479401
JournalBiochim Biophys Acta
Year2002
Volume1599
Pages9-20
AuthorsHurlbert JC, Preston JF 2nd
TitleDifferences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
[17]
PubMed ID11852237
JournalTrends Biochem Sci
Year2002
Volume27
Pages59-62
AuthorsCiccarelli FD, Copley RR, Doerks T, Russell RB, Bork P
TitleCASH--a beta-helix domain widespread among carbohydrate-binding proteins.
[18]
PubMed ID12540845
JournalJ Biol Chem
Year2003
Volume278
Pages12271-7
AuthorsHerron SR, Scavetta RD, Garrett M, Legner M, Jurnak F
TitleCharacterization and implications of Ca2+ binding to pectate lyase C.
Related PDB1o88,1o8d,1o8e,1o8f,1o8g,1o8h,1o8i,1o8j,1o8k,1o8l,1o8m

comments
This enzyme is homologous to the enzyme (S00546 in EzCatDB).
According to the literature [8], the catalytic reaction (beta-elimination) involves three process:
(1) Neutralization of the carboxyl group adjacent to the deprotonation site of leaving group.
(2) Deprotonation at the C-5 atom (deprotonation site of leaving group).
(3) Protonation to the glycosidic oxygen (eliminated group).
Although calcium ion usually plays a structural role, it is catalytically importnat in this enzyme. The calcium ion at the active site seems to acidify (or lower the pKa of) the alpha-proton at C-5 atom for abstraction by a general base, by polarizing and neutralizing the carboxy group (or uronic acid group) of the substrate (see [4], [5] & [6]). Here, the calcium ion acts as a Lewis acid.
The literature [8] proposed that the conserved residue, Arg218 (of 1air), might serve as a general base, to abstract the proton at the C-5 atom. Although it is unusual for argnine residues to be a general base, the substrate carboxylate group (uronic acid) makes Arg218 to act as a general base, by lowering its pKa. As for the general acid, which protonates the glycosidic oxygen atom, a water molecule was suggested by the paper [8]. No alternative group has been found for this role.
Moreover, during the catalysis, an enolic intermediate is formed and stabilized by Lys190 (of 1air) (see [8]).

createdupdated
2004-04-042009-03-27
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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